In recent years, as a result of the development of three-dimensional culturing technology and clearing technology, the need for microscopes that enable three-dimensional observation of a wide field of view is increasing. A known example of such microscopes is disclosed in PTL 1. In the microscope system disclosed in PTL 1, a plurality of partial image groups with various image-acquisition positions in the depth direction of the specimen are acquired only at the position where a specimen container is mounted, and the plurality of partial image groups are combined into a map image.